program for microRNA (miRNA) target prediction

I am trying to identify a micro RNA that targets our gene of interest. I'm finding it hard to determine whether the micros that i have cloned are specific to our region due to a lack of sequence alignment programmes that allow for the mismatches and gaps that occur between micro RNAs and their targets.

Basically....what is a good programme to align micro RNAs with potential targets?

I found the program miRanda is the best one. It needs local installation.

miRanda is an algorithm for finding genomic targets for microRNAs. This algorithm has been written in C and is available as an open-source method under the GPL. MiRanda was developed at the Computational Biology Center of Memorial Sloan-Kettering Cancer Center.

Could anyone tell me how to install and use miRanda software?
I am using Windows XP computer, and had installed J2SE 5.0. But when opening miRanda v1.0b, the program says error, although MiRanda Java Interface v1.0 window opens. Further I have no idea how to use it. Does this software already have miRNA library, or should I make it like mouse miRNAs, human RNAs...?

If the java interface doesn't work, try the command line version. You just launch a command window by going to start->run and type cmd, then go to the folder where mirnada resides. Before you run the program you have to create two FASTA files one holding your miRNA, the other holding the sequences to be scanned. Then type miranda mirna_file sequence_file output_file. There is a detailed instruction coming with the download.